CentroidHomfold-LAST: Accurate prediction of RNA secondary structure using automatically collected homologous sequences

Nucleic Acids Research

Volumn 39, Issue SUPPL. 2, 2011, Pages

  Hamada, Michiaki ^a,b   Yamada, Koichiro ^c   Sato, Kengo ^a   Frith, Martin C ^b   Asai, Kiyoshi ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c Information and Mathematics Science Laboratory Inc   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; BIOINFORMATICS; GENETIC ALGORITHM; INTERMETHOD COMPARISON; INTERNET; PREDICTION; PRIORITY JOURNAL; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

INTERNET; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE ANALYSIS, RNA; SEQUENCE HOMOLOGY, NUCLEIC ACID; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 79960025412     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr290     Document Type: Article

References (26)

1. Mattick, J.S. and Makunin, I.V. (2006) Non-coding RNA. Hum. Mol. Genet., 15, 17-29.
2. Do, C., Woods, D. and Batzoglou, S. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98. (Pubitemid 44288277)
3. Hamada, M., Kiryu, H., Sato, K., Mituyama, T. and Asai, K. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25, 465-473.
4. Markham, N. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
5. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31, 3406-3415. (Pubitemid 37442169)
6. Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, S., Tacker, M. and Schuster, P. (1994) Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125, 167-188.
7. Mathews, D., Disney, M., Childs, J., Schroeder, S., Zuker, M. and Turner, D. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292. (Pubitemid 38638025)
8. Hamada, M., Kiryu, H., Iwasaki, W. and Asai, K. (2011) Generalized centroid estimators in bioinformatics. PLoS ONE, 6, e16450.
9. Bernhart, S., Hofacker, I., Will, S., Gruber, A. and Stadler, P. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474.
10. Hamada, M., Sato, K. and Asai, K. (2011) Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res., 39, 393-402.
11. Seemann, S., Gorodkin, J. and Backofen, R. (2008) Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res., 36, 6355-6362.
12. Hamada, M., Sato, K., Kiryu, H., Mituyama, T. and Asai, K. (2009) Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics, 25, i330-i338.
13. Frith, M.C., Hamada, M. and Horton, P. (2010) Parameters for accurate genome alignment. BMC Bioinformatics, 11, 80.
14. Kielbasa, S.M., Wan, R., Sato, K., Horton, P. and Frith, M. (2011) Adaptive seeds tame genomic sequence comparison. Genome Res., 21, 487-493.
15. Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
16. Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431. (Pubitemid 37442172)
17. Andronescu, M., Condon, A., Hoos, H., Mathews, D. and Murphy, K. (2007) Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics, 23, 19-28.
18. Ding, Y., Chan, C.Y. and Lawrence, C.E. (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res., 32, W135-W141. (Pubitemid 38997315)
19. Sankoff, D. (1985) Simultaneous solution of the RNA folding alignment and protosequence problems. SIAM J. Appl. Math, 45, 810-825. (Pubitemid 15563502)
20. McCaskill, J.S. (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers, 29, 1105-1119. (Pubitemid 20145703)
21. Do, C., Gross, S. and Batzoglou, S. (2006) Contralign: Discriminative training for protein sequence alignment. In Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A. and Waterman, M.S. (eds), RECOMB, Vol. 3909 of Lecture Notes in Computer Science. Springer, pp. 160-174. (Pubitemid 44019154)
22. Andronescu, M., Condon, A., Hoos, H.H., Mathews, D.H. and Murphy, K.P. (2010) Computational approaches for RNA energy parameter estimation. RNA, 16, 2304-2318.
23. Do, C., Mahabhashyam, M., Brudno, M. and Batzoglou, S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340. (Pubitemid 40309398)
24. Sheetlin, S., Park, Y. and Spouge, J.L. (2005) The Gumbel pre-factor k for gapped local alignment can be estimated from simulations of global alignment. Nucleic Acids Res., 33, 4987-4994. (Pubitemid 41418897)
25. Huang, Y., Niu, B., Gao, Y., Fu, L. and Li, W. (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences. Bioinformatics, 26, 680-682.
26. Sato, K., Hamada, M., Asai, K. and Mituyama, T. (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res., 37, W277-W280.